{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T12:15:06Z","timestamp":1756901706195,"version":"3.44.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T00:00:00Z","timestamp":1756252800000},"content-version":"vor","delay-in-days":57,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFC2701201"],"award-info":[{"award-number":["2021YFC2701201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32250710678","32370630"],"award-info":[{"award-number":["32250710678","32370630"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Three-dimensional (3D) genomic architecture is crucial for the regulation of different biological processes, and the study of multi-way chromatin structures represents a cutting-edge area in this field. Pore-C is an advanced experimental technique integrating chromosome conformation capture (3C) with Nanopore long-read sequencing, which can effectively capture complex multi-way chromatin contacts across the genome. Due to the absence of comprehensive and dedicated tools, the analysis of Pore-C data remains challenging, restricting its broader application. To address this limitation, we developed Pore-C Pipeline Toolbox (PPL-Toolbox), a specialized software for a comprehensive analysis of multi-way chromatin interactions from Pore-C data. PPL-Toolbox incorporates a suite of optimized modules, including quality control, multi-way interaction extraction, noise reduction for multi-way contacts, advanced visualization tools for multi-way contacts, and haplotype map generation. Evaluation on both simulated and real datasets demonstrates that the PPL-Toolbox outperforms existing methods by providing a more comprehensive set of results. PPL-Toolbox is expected to become a powerful and versatile tool, driving advance in multi-way 3D genomics research, and enabling new discoveries in the field. PPL-Toolbox is publicly available on GitHub (https:\/\/github.com\/versarchey\/PPL-Toolbox).<\/jats:p>","DOI":"10.1093\/bib\/bbaf435","type":"journal-article","created":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T11:12:26Z","timestamp":1756293146000},"source":"Crossref","is-referenced-by-count":0,"title":["Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-6975-6078","authenticated-orcid":false,"given":"Zhenji","family":"Wang","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2556-8619","authenticated-orcid":false,"given":"Qiangqiang","family":"Fu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6944-8244","authenticated-orcid":false,"given":"Fuming","family":"Lai","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7948-177X","authenticated-orcid":false,"given":"Qiangwei","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6075-0768","authenticated-orcid":false,"given":"Yaping","family":"Fang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1601-6640","authenticated-orcid":false,"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","place":["China"]},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 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